Defect lines of EER movies

Import and Export
#1

We recently acquired small data using Falcon 4. Interestingly, after importing EER movies into cryoSPARC, we recognized a kind of artifact showing two vertical lines as shown in the attachment (dead pixel columns?). Does anyone know how to figure out defect lines when importing EER movies into cryoSPARC?

P47_J2_raw_data_j2importedfoilhole_18833600_data_16747122_16747124_20210220_065731_eereer
P47_J2_raw_data_j2importedfoilhole_18833600_data_16747122_16747124_20210220_065731_eereer1024×1024 608 KB

#2

Hi @xtalee,

Thanks for posting. EER data should come with a gain reference (.gain format probably, or .mrc format) and in the gain reference, any zero values indicate defects. These are automatically corrected during motion correction. However, the import job (presumably this image is from the import job?) does not actually correct the defects in the images it creates. If you run the data through motion correction (eg. patch motion) you should see that the defects disappear in the motion corrected micrographs (and you can check with the exposure curation job for example).
This assumes that the gain reference actually does have zeros in the defect locations (which is part of the EER spec from TFS).

Let us know what happens!

#3

Hi @apunjani,

Thank you for letting me know your thoughts. Although the EER movies are imported with a gain reference (mrc format), the defects still appear in the motion corrected micrographs when I check with the exposure curation job.

index
index1024×1024 618 KB

#4

Hi @xtalee,

Thanks for replying. Do you then have a separate defect file?
Can you check if the gain reference actually does have zero values in the defect positions?

#5

Hello,

I am having this same issue. Was there any solution in the end?

Thanks in advance.